Recently published apps

We have published the following apps in our Public Apps gallery:

• Cyrius (v1.1.1, CWL1.2), a tool that genotypes CYP2D6 in WGS data. It takes WGS BAM or CRAM files and creates a TSV report with CYP2D6 alleles.
• Two PharmCAT (v1.6.0, CWL1.2) tools:
  • PharmCAT VCF Preprocess is a tool that takes a VCF file and prepares it for downstream processing with PharmCAT, and
  • PharmCAT, a tool for interpreting guideline variants in VCF files.
• Two Biobambam2 (v2.0.183, CWL1.2) tools:
  • Biobambam2 Bamtofastq that converts BAM/CRAM/SAM files to FASTQ format, and
  • Biobambam2 Bamseqchksum – tool for calculating hashes for the contents of the provided alignments file.
• Two Cojac (v0.2, CWL1.2) tools:
  • Cojac cooc-mutbamscan is a tool that scans amplicons for mutation co-occurrence, and
  • Cojac cooc-tabmut converts Cojac cooc-mutbamscan results (JSON, YAML) to a CSV file.
• Six iVar (v1.3.1, CWL1.2) tools:
  • iVar trim takes a sorted BAM file and trims reads based on quality and primers if provided.
  • iVar variants takes an aligned BAM file and a Reference sequence and produces a TSV file with detected variants.
  • iVar filtervariants filters variants across provided TSV replicate or sample variant files.
  • iVar consensus takes an aligned BAM file and generates a FASTA file with consensus sequences and a TXT file with average base qualities.
  • iVar getmasked takes a TSV file with variants generated by iVar tools, Primers BED file, and a TSV file with primer pair information and retrieves primers with mismatches to the reference sequence. Please note that this tool is only applicable to amplicon-based sequencing.
  • iVar removereads takes a BAM file trimmed with iVar trim, a Primers BED file, and the Mismatch primer indices output by iVar getmasked and removes reads associated with identified mismatched primers.
• Pangolin (v40.5, CWL1.2) (Phylogenetic Assignment of Named Global Outbreak LINeages), is a tool that takes a FASTA file with SARS-CoV-2 sequences and assigns each sequence to a Pango lineage using PangoLEARN.
• Picard RevertSam (v2.25.7, CWL1.2), is a tool that reverts a BAM/SAM file to a previous state. It can be used to recreate an unaligned BAM file from aligned BAM/SAM files or restore original qualities to post-BQSR files (if original qualities were stored).

Marko Marinkovic